jashephe's comments

It sounds like you want a dictation mic. Philips’s SpeechMike and OM System’s (formerly Olympus) RecMic are big in the healthcare space. My SpeechMike is wireless with a USB dongle and has something akin to a trackpoint for mouse movement, and buttons that can be programmed to send keystrokes.

Dictation mics are not cheap, unfortunately, but you may be able to get used ones for much less.

The periodic table poster under "High binding problems" is billed as evidence of model limitations, but I wonder if it just suggests that 4o is a fan of "Look Around You".

I'm a little disappointed that their linked preprint doesn't appear to include any molecular biology; i.e. they don't actually try to synthesize any of their predicted sequences and test function. It wouldn't be an outrageous synthesis task to make some of the CRISPR-Cas sequences they generated.

Also interesting that AlphaMisense is omitted from Figure 2B; it substantially outperforms the ESM-based ESM1b in our hands. But I guess the idea is that this is a general-purpose DNA language model whereas AlphaMissense is domain-specific for variant effect prediction?

A tangent: does anyone have recommendations for a library for easy Swift-Rust interop? This is a cool tool, but I’d much rather make a GUI natively with e.g. SwiftUI and then call out to Rust for business logic. The previous times I’ve looked into this, both languages had to communicate through a C intermediate, and handling more complex types became a chore…

All sorts of offtopic prompts are unsurprisingly generating nonsensical answers, but even prompting with "lecture notes on clathrin-mediated endocytosis" yielded:

"In the case of clathrin-mediated endocytosis, it is a process used by eukaryotic cells to take up extracellular material and molecules into the cell. It is a mechanism used by cells to take up specific molecules, and it is a mechanism used by cells to regulate the composition of the cell surface. It is a mechanism used by cells to regulate the composition of the cell surface, and it is a mechanism used by cells to take up specific molecules. It is a mechanism used by cells to take up specific molecules. It is a mechanism used by cells to take up specific molecules, and it is a mechanism used by cells to take up specific molecules."

Global models of gene expression for an entire cell are fairly distant at this point, but there is quite a bit of work into modeling transcriptional activity from sequence. If you're interested in reading more, a relevant technology to search for would be the "Massively Parallel Reporter Assay", or MPRA, which couples pools of 10⁴–10⁵+ synthetic DNA sequences with RNA sequencing to measure transcriptional output. Data from MPRA experiments is being used to train models, although these models are not anywhere near a point where you could model the gene expression of all regulatory elements in a cell; they are usually focused on a specific factor or regulatory sequence.

I'm confused. Where does this say the vaccine is mRNA? The Valneva VLA15 website explicitly states "VLA15 is a multivalent recombinant protein vaccine" [1], and the linked press release calls it a "investigational multivalent protein subunit vaccine". Does nobody actually read these things?

See [2], "Subunit Vaccines".

[1] https://valneva.com/research-development/lyme-disease/

[2] https://www.niaid.nih.gov/research/vaccine-types

Not sure why a direct quote from the article is getting so heavily downvoted. Maybe there’s something here, but if the variants were in the published paper, it doesn’t really matter if the raw sequences were yanked off of the SRA.

Taum Sauk is unusual in that the dam fully surrounds the upper reservoir (i.e. the lake was made from scratch), although certainly all types of dam can fail.

I'd be quite interested to see if there's any correlation between Valisure's measurements and time elapsed since manufacture for each lot.

Isn't pumped storage hydro kind of that "silver bullet"? At least in places with the right geography?

Indeed. Maybe someone with more expertise can chime in — it's not clear to me if getting a vaccine with the chimp adenovirus backbone would preclude the possibility of getting another vaccine based on that backbone in the future (because of immunity to the backbone).

Based on this NYT article [1], some logistics companies planning to store and transport the vaccine are using freezers from Stirling Ultracold. It may just be a curiosity, but their freezers (as the name would suggest) use bona fide Stirling engines rather than the typical two-stage compressors used in most ULT freezers.

As someone in life science research who uses plenty of -80 freezers, I've always been curious about Stirling Ultracold. Maybe they're on to something after all.

[1] https://www.nytimes.com/2020/09/18/business/coronavirus-covi...

It’s always surprising to me to see an article like this that’s vaguely about a person, without seemingly any attempts to reach that person for comment. I’ve filed issued on a few of Michael’s repositories since he left Apple, and he was extremely responsive. I’d be surprised if he ignored Phoronix if they had actually reached out to him.

While "Heroes of CRISPR" is a fairly detailed history of the whole affair, it's always worth noting that it was written by Eric Lander, the director of an institute with a strong vested financial interest in having the story interpreted in a particular way.

Indeed. In Chadwick Boseman’s case, the onset was at _such_ a young age that it suggests (total speculation) he might have had a hereditary cancer syndrome or some other familial risk factor. More widespread genetic testing may help people like him in the future.

Just to clarify — the vaccine uses as its backbone a type of adenovirus that typically infects chimpanzees, modified by the addition of pieces from SARS-CoV-2, but the experiments testing efficacy are performed in mice (specifically, a type of mice engineered to express humanized ACE2).

This vaccine has not been tested in chimpanzees (and actually such experiments would probably be a challenge, since they may have existing immunity to the backbone adenovirus).

(edit: parent comment initially mentioned experiments in chimpanzees rather than mice)

The above is a good example of how results can be "wrong" in theory papers, but I work in an experimental field of research and at least in my world, having a paper present results that turn out to be wrong isn't really all that surprising. Experimental papers aren't proof of phenomena as much as they're an attempt to persuade you of the authors' worldview, which may or may not turn out to be correct in hindsight. This isn't grounds for retraction — there are plenty of well-intentioned and reasonably-interpreted experiments that end up not holding up as the field moves forward.

Again, not saying that papers can't have problems with methodology, assumptions, or — particularly in the case of theory — soundness, but sometimes, "good" papers can be wrong. These papers sit in the body of literature, and are important context for modern findings. I do wonder if there could be some way to indicate to readers without domain-specific expertise that such a paper has been superseded, so to speak.

This calls to mind the ever-relevant “Science: The Endless Frontier” [1] by Vannevar Bush, who more or less oversaw the entire American federal research enterprise during and post-WWII. He famously said that the best thing you can do for scientific progress is give scientists money and then get out of the way (i.e. not even putting out requests for grant submissions in specific domains, like the NIH often does now).

[1] https://www.nsf.gov/od/lpa/nsf50/vbush1945.htm

Oh, absolutely. I guess I was wondering if accusations alone would serve to substantially inconvenience or embitter individual scientists, or decrease public trust in academic research and academicians in general. Not trying to suggest that this case specifically is some foreign plot.